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Archive for the ‘Population Health Management, Genetics & Pharmaceutical’ Category


Approaches and Solutions for Management of the COVID Pandemic

Reporter: Aviva Lev- Ari, PhD, RN and Stephen J. Williams, PhD  
 
 
 
 
 
October 8, 2020 N Engl J Med 2020; 383:1479-1480 DOI: 10.1056/NEJMe2029812

 

Dying in a Leadership Vacuum

CONTINUE TO READ AT THE SOURCE N Engl J Med 2020; 383:1479-1480 DOI: 10.1056/NEJMe2029812   Janice Hopkins Tanne. (2020) Covid 19: NEJM and former CDC director launch stinging attacks on US response. BMJ, m3925. BMJ 2020;371:m3925

Covid 19: NEJM and former CDC director launch stinging attacks on US response

Janice Hopkins Tanne Author affiliations

The US is “dying in a leadership vacuum,” in responding to the covid-19 pandemic, the New England Journal of Medicine has said in an editorial.

“Our leaders have failed. They have taken a crisis and turned it into a tragedy,” the NEJM editors said. US leaders are “dangerously incompetent,” have undercut trust in science and in government,” and should be voted out,1 the journal said.

The intervention came as a former director of the Centers for Disease Control and Prevention (CDC) suggested the current CDC director should update staff in writing about the agency’s failings, apologise, and resign.23

The US leads the world in the death rate from covid-19, which is far higher than larger countries and those with less sophisticated technology and health services, the editors said.

“We have failed at almost every step,” they wrote, describing problems with supplies of personal protective equipment, delays in testing, and failure to employ quarantine, isolation, and social distancing appropriately and quickly. Government inaction has led to business losses and unemployment.

Earlier, William Foege, former director of the CDC and a leader in smallpox eradication, criticised the US response and the failure of the CDC. He sent a letter to Robert Redfield, the current CDC director, asking him to write to CDC employees describing the White House’s failure to put the CDC in charge of the covid-19 pandemic and then resign. A letter, he wrote, would be on the record.

Foege called the US response to the pandemic “a slaughter and not just a political dispute” that had turned the CDC’s reputation from “gold to tarnished brass.”

Foege is emeritus presidential distinguished professor of international health at Emory University. He was director of the Carter Center’s Task Force for Child Survival and senior medical advisor to the Bill and Melinda Gates Foundation. President Barack Obama awarded him the Presidential Medal of Freedom, the nation’s highest civilian honour, in 2012. His private letter, written on 23 September, was published by USA Today on 7 October.

Redfield, a virologist with expertise in HIV/AIDS and a clinician, served in the US Army’s medical corps. He co-founded the University of Maryland’s Institute of Human Virology and was chief of infectious diseases at the university’s medical school.

Foege wrote, “You don’t want to be seen, in the future, as forsaking your role as servant to the public in order to become a servant to a corrupt president. You could send a letter to all CDC employees (a letter leaves a record and avoids the chance of making a mistake with a speech) laying out the facts. The White House will, of course, respond with fury. But you will have right on your side. Like Martin Luther, you can say, ‘Here I stand, I cannot do otherwise.’”

Among the truths that need to be faced, Foege said, are that, despite White House spin attempts, the failure of the US public health system is because of “the incompetence and illogic of the White House programme.”

The White House failed to put the CDC in charge of the pandemic, violating rules of public health so that “people and the media go to the academic community for truth, rather than to CDC,” Foege’s letter says. Unlike former responses to health crises, there has been no federal plan, “resulting in 50 states developing their own plans, often in competition.”

The need to form coalitions to fight the pandemic “has been ignored as the president thrives instead on creating divisions, and the need for global cooperation has been squandered by an ‘America first’ policy. The best decisions are based on the best science while the best results are based on the best management. The White House has rejected both science and good management,” Foege wrote.

Foege, the CDC, Redfield, and the White House have not publicly commented on the letter.

References
  SOURCES for the NEJM https://www.nejm.org/doi/full/10.1056/NEJMe2029812?query=recirc_mostViewed_railB_article https://www.nejm.org/doi/full/10.1056/NEJMe2029812#.X39d2y9tN84.twitter Janice Hopkins Tanne. (2020) Covid 19: NEJM and former CDC director launch stinging attacks on US response. BMJ, m3925. BMJ 2020;371:m3925

Covid 19: NEJM and former CDC director launch stinging attacks on US response

BMJ 2020371 doi: https://doi.org/10.1136/bmj.m3925 (Published 08 October 2020) Cite this as: BMJ 2020;371:m3925   References
  1. Johns Hopkins University Coronavirus Resource Center. COVID-19 dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (https://coronavirus.jhu.edu/map.html. opens in new tab).

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  2. Total number of COVID-19 tests per confirmed case, September 14, 2020. Our World in Data (https://ourworldindata.org/grapher/number-of-covid-19-tests-per-confirmed-case. opens in new tab).

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  3. McGinley L, Abutaleb L, Johnson CY. Inside Trump’s pressure campaign on federal scientists over a Covid-19 treatment. Washington Post. August 302020 (https://www.washingtonpost.com/health/convalescent-plasma-treatment-covid19-fda/2020/08/29/e39a75ec-e935-11ea-bc79-834454439a44_story.html. opens in new tab).

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  4. Haberman M. Trump admits downplaying the virus knowing it was ‘deadly stuff.’ New York Times. September 92020 (https://www.nytimes.com/2020/09/09/us/politics/woodward-trump-book-virus.html. opens in new tab).

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Related Articles

 

Other related articles published in this Open Access Online Scientific Journal include the following EIGHT topics we cover since March 14, 2020 on LPBI Group’s Coronavirus PORTAL

https://pharmaceuticalintelligence.com/coronavirus-portal/

Eight COVID-19 Topics Covered and Lead Curators are:

  1. Breakthrough News Corner
  2. Development of Medical Counter-measures for 2019-nCoV, CoVid19, Coronavirus
  3. An Epidemiological Approach Stephen J. Williams, PhD and Aviva Lev-Ari, PhD, RN Lead Curators – e–mail Contacts: sjwilliamspa@comcast.net and avivalev-ari@alum.berkeley.edu
  4. Community Impact Stephen J. Williams, PhD and Irina Robu, PhD Lead Curators – e–mail Contacts: irina.stefania@gmail.com and sjwilliamspa@comcast.net
  5. Economic Impact of The Coronavirus Pandemic Dr. Joel Shertok, PhD Lead Curator – e–mail Contact: jshertok@processindconsultants.com
  6. Voices of Global Citizens: Impact of The Coronavirus Pandemic, Gail S. Thornton, M.A. Lead Curator – e–mail Contact: gailsthornton@yahoo.com
  7. Diagnosis of Coronavirus Infection by Medical Imaging and Cardiovascular Impacts of Viral Infection, Aviva Lev-Ari, PhD, RN Lead Curator e-mail contact: avivalev-ari@alum.berkeley.edu
  8. Key Opinion Leaders Followed by LPBI Aviva Lev-Ari, PhD, RN and Dr. Ofer Markman, PhD Lead Curators e-mail contacts: oferm2015@gmail.com and avivalev-ari@alum.berkeley.edu

 

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The lessons from the Covid-19 response, according to Anthony Fauci

Reporter : Irina Robu, PhD

 

UPDATED on 10/18/2020

 

 

Since COVID-19 was declared an international pandemic, the world has learned difficult lessons according to Dr. Anthony Fauci. They are as follows:

  • Don’t understand the impact of the pandemic. Don’t ever estimate [an outbreak] as it evolves and don’t try to look at the rosy side of things.
  • Always do scientifically sound research.
  • Adapt to new information. If you look at what we knew in February compared to what we know now [about Covid-19], there really are a lot of differences. The role of masks, the role of aerosol, the role of indoor vs. outdoors, closed spaces. You’ve just got to be humble enough to realize that we don’t know it all from the get-go and even as we get into it.
  • Address existing health care disparities. There is a high number of hospitalizations with COVID within African-American and Latin community.

SOURCE

https://www.statnews.com/2020/09/10/anthony-fauci-lessons-learned-covid19-pandemic

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Detecting SARS-COV-2 antibodies in serum and plasma samples

Reporter: Irina Robu, PhD

Convalescent plasma therapy is a possible treatment under investigation where antibodies from recovered patients are transfused to current COVID-19 patients with the intent to help them fight the infection and buy time until their immune system can produce antibodies. Yet, not all recovered patients have the same quantity of antibody titers suitable for such transfusions. In some patients it will minimize the severity of the disease length.

The U.S. Food and Drug Administration authorized convalescent plasma therapy for patients with coronavirus disease 2019 and it permitted to be used during the pandemic because there is no approved treatment for COVID-19. The donated blood is processed to remove cells, leaving behind liquid and antibody.   

Companies like Forte Bío are developing instruments such as Octet HTX Instrument, Octet RED384 Octet RED96e Instrument and Octet K2 Instrument to detect SARS-COV-2 antibodies in serum and plasma samples. The Octet technology allows quantification with high resolution comparable to an HPLC . The instrument utilizes BLI enabling label-free detection for protein quantitation and kinetic characterization at unmatched speed and throughput. The instrument can  measure up to 96 samples simultaneously allowing both unlimited characterization capacity for various applications and custom assay tailoring to maximize analytical throughput or sensitivity and preventing bottlenecks. 

 How are antibodies tested ?

  1. Immobilize a virus protein such as the receptor binding domain (RBD) of the SARS CoV-2 spike protein.
  2. Dip the coronavirus biosensor into diluted patient plasma or serum samples.
  3. Block the biosensor with non-relevant serum or blocking buffer if needed to prevent non-specific binding.

Even the researchers believe that the risk to donors is low, there are additional risks such as allergic reactions, lung damage, difficulty breathing or infections such as HIV, hepatitis B and Donated blood must be tested for safety prior to administering to patients.

What to expect ? It is up to the doctor treating the patient, if convalescent plasma therapy is an option.  Even though data from clinical trials suggest that convalescent plasma may diminish the severity or duration of the COVID19, more research is needed to determine if convalescent plasma therapy is an effective treatment.

SOURCE

https://www.fortebio.com/covid19research19research

https://www.medrxiv.org/content/10.1101/2020.07.17.20156281v1

 

Other related articles were published in this Open Access Online Scientific Journal including the following:

https://pharmaceuticalintelligence.com/2020/05/18/race-to-develop-antibody-drugs-for-covid-19

https://pharmaceuticalintelligence.com/2020/05/18/race-to-develop-antibody-drugs-for-covid-19

 

 

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Why Do Some COVID-19 Patients Infect Many Others, Whereas Most Don’t Spread the Virus At All?

Guest Reporter: Jason S Zielonka, MD

One of the key parameters in COVID-19 pandemic epidemiology has been to define the spread metrics, basically identifying how a host spreads the virus to uninfected individuals. The pattern of spread can impact how and which preventative measures such as social distancing and hand washing can impact spread patterns. In particular, two metrics, the average number of new patients infected by each host (the reproduction number, R) and a factor representing the tendency to cluster (the dispersion factor, k) can be used to describe and model the spread of a virus quite well. Higher values of R mean more people are infected by a single host, i.e, the disease is more contagious; lower values of k mean that a host infects a larger number of new patients, i.e., the disease is more clustered.

The reproduction number, R, for SARS-CoV-2, without social distancing, is about 3. But this is an average, taken over an aggregate of patients. For most individuals, R is zero, i.e., most patients do not transmit the virus to others. For comparison, SARS and MERS, both coronaviruses, had R > 3 and the 1918 influenza pandemic had R >> 3. So what determines viral spread and how can we use that information to treat and eradicate SARS-CoV-2?

In 2005, by modeling the Chinese SARS outbreak and comparing the model to the real-world data, Lloyd-Smith and co-authors were able to determine that SARS had a k of about 0.16. MERS, in 2012, was estimated to have k around 0.25; the 1918 pandemic, by contrast, had a k of 1, meaning it had very little cluster effect. The current modeling indicates that k for SARS-CoV-2 is not conclusive, but it appears higher than k for either SARS or MERS.

This work has provided insights into some of the factors influencing cluster spread, which can be controlled in a more specific way than quarantining an entire population. There will be individual variance, but we know that people are particularly infectious over a certain time period; that certain activities are more conducive to droplet formation and wider spread, and that being outdoors rather than in confined and noisy indoor locations leads to less spread. This can all lead to better, faster and more tolerable approaches to either future pandemics or to a recurrence of SARS-CoV-2.

SOURCE

https://www.sciencemag.org/news/2020/05/why-do-some-covid-19-patients-infect-many-others-whereas-most-don-t-spread-virus-all

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From AAAS Science News on COVID19: New CRISPR based diagnostic may shorten testing time to 5 minutes

Reporter: Stephen J. Williams, Ph.D.

 

 

 

 

 

 

 

 

 

A new CRISPR-based diagnostic could shorten wait times for coronavirus tests.

 

 

New test detects coronavirus in just 5 minutes

By Robert F. ServiceOct. 8, 2020 , 3:45 PM

Science’s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.

 

Researchers have used CRISPR gene-editing technology to come up with a test that detects the pandemic coronavirus in just 5 minutes. The diagnostic doesn’t require expensive lab equipment to run and could potentially be deployed at doctor’s offices, schools, and office buildings.

“It looks like they have a really rock-solid test,” says Max Wilson, a molecular biologist at the University of California (UC), Santa Barbara. “It’s really quite elegant.”

CRISPR diagnostics are just one way researchers are trying to speed coronavirus testing. The new test is the fastest CRISPR-based diagnostic yet. In May, for example, two teams reported creating CRISPR-based coronavirus tests that could detect the virus in about an hour, much faster than the 24 hours needed for conventional coronavirus diagnostic tests.CRISPR tests work by identifying a sequence of RNA—about 20 RNA bases long—that is unique to SARS-CoV-2. They do so by creating a “guide” RNA that is complementary to the target RNA sequence and, thus, will bind to it in solution. When the guide binds to its target, the CRISPR tool’s Cas13 “scissors” enzyme turns on and cuts apart any nearby single-stranded RNA. These cuts release a separately introduced fluorescent particle in the test solution. When the sample is then hit with a burst of laser light, the released fluorescent particles light up, signaling the presence of the virus. These initial CRISPR tests, however, required researchers to first amplify any potential viral RNA before running it through the diagnostic to increase their odds of spotting a signal. That added complexity, cost, and time, and put a strain on scarce chemical reagents. Now, researchers led by Jennifer Doudna, who won a share of this year’s Nobel Prize in Chemistry yesterday for her co-discovery of CRISPR, report creating a novel CRISPR diagnostic that doesn’t amplify coronavirus RNA. Instead, Doudna and her colleagues spent months testing hundreds of guide RNAs to find multiple guides that work in tandem to increase the sensitivity of the test.

In a new preprint, the researchers report that with a single guide RNA, they could detect as few as 100,000 viruses per microliter of solution. And if they add a second guide RNA, they can detect as few as 100 viruses per microliter.

That’s still not as good as the conventional coronavirus diagnostic setup, which uses expensive lab-based machines to track the virus down to one virus per microliter, says Melanie Ott, a virologist at UC San Francisco who helped lead the project with Doudna. However, she says, the new setup was able to accurately identify a batch of five positive clinical samples with perfect accuracy in just 5 minutes per test, whereas the standard test can take 1 day or more to return results.

The new test has another key advantage, Wilson says: quantifying a sample’s amount of virus. When standard coronavirus tests amplify the virus’ genetic material in order to detect it, this changes the amount of genetic material present—and thus wipes out any chance of precisely quantifying just how much virus is in the sample.

By contrast, Ott’s and Doudna’s team found that the strength of the fluorescent signal was proportional to the amount of virus in their sample. That revealed not just whether a sample was positive, but also how much virus a patient had. That information can help doctors tailor treatment decisions to each patient’s condition, Wilson says.

Doudna and Ott say they and their colleagues are now working to validate their test setup and are looking into how to commercialize it.

Posted in:

doi:10.1126/science.abf1752

Robert F. Service

Bob is a news reporter for Science in Portland, Oregon, covering chemistry, materials science, and energy stories.

 

Source: https://www.sciencemag.org/news/2020/10/new-test-detects-coronavirus-just-5-minutes

Other articles on CRISPR and COVID19 can be found on our Coronavirus Portal and the following articles:

The Nobel Prize in Chemistry 2020: Emmanuelle Charpentier & Jennifer A. Doudna
The University of California has a proud legacy of winning Nobel Prizes, 68 faculty and staff have been awarded 69 Nobel Prizes.
Toaster Sized Machine Detects COVID-19
Study with important implications when considering widespread serological testing, Ab protection against re-infection with SARS-CoV-2 and the durability of vaccine protection

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Tiny biologic drug to fight COVID-19 show promise in animal models

Reporter : Irina Robu, PhD

A research team at University of Pittsburg School of Medicine identified an antibody component that is 10 times smaller than a full-sized antibody. Their research published in Cell, indicates that the drug, Ab8 based on it is effective in mice and hamsters. The research was started by screening a library of about 100 billion antibody fragments to identify candidates that bound tightly to the spike protein on SARS-CoV-2’s surface, which the virus uses to enter and infect human cells.

A typical antibody consists of two heavy chains and two light chains. The chosen molecule is the variable domain of the heavy chain of an immunoglobulin, which is a type of antibody. The heavy chain variable domain is essential for binding with an antigen. Ab8 was created by fusing the variable, heavy chain domain with part of the immunoglobulin tail region, giving it immune functions but doing so with a molecule that’s about half the size of a full immunoglobulin.

The smaller size of the antibody can improve the therapeutic efficacy for infectious diseases and can be delivered through inhalation. Their research showed that Ab8 completely neutralized SARS-CoV-2 in lab dishes. The drug developed showed that inhibited the virus in lung tissue in animal body even at the lowest dose 2 mg/kg as compared to untreated controls.

The research team is looking to determine the drug effect in hamsters, which were reported to have better clinical signatures of COVID-19. And the hamsters that got the drug display less severe pneumonia that did the control animals. Drugs with alternative administration routers could provide additions to the first wave of COVID-19 therapies and vaccines.

What is more important, Ab8 does not appear to bind to human cells which is a good sign that it won’t have negative side effects.

SOURCE

https://www.fiercebiotech.com/research/small-sized-biologic-against-covid-19-shows-promise-animal-models

 

 

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Llama inspired “AeroNabs” to strangle COVID-19 with an inhaler 

Reporter : Irina Robu, PhD

Llama and other camelids fight off pathogens like viruses with tiny antibodies called nanobodies. A USCF team used protein engineering to make a synthetic nanobody that prevents the spike protein on the surface of SARS-CoV-2 from binding to healthy cells and infecting them. The team indicates promising preclinical results for aerosol formulation and can be used as a self-administered form of protein against the virus.

According to the UCSF team, an aerosolized form of nanobody exhibit SARS-CoV-2 incapable of binding to the ACE2 receptor on healthy cells that line airways. The synthetic nanobody stays functional after it was freeze-dried, exposed to heat and aerosolized.

The researchers ongoing screening a library of synthetic nanobodies, ultimately landing on 21 that banned the spike-ACE2 interaction. The scientists decided that in order to be truly efficient, a nanobody based treatment with interact with all three of the receptor binding domains on the spike protein that attaches to ACE2.  Their solution was to engineer a molecular chain that connects three nanobodies together, which would ensure that when one of the nanobodies attached to RBD, the others would link to the two remaining RBD. This molecular chain resulted in a drug candidate proved to be 200,000 times more potent than a single antibody.

At the same time, ExeVir Bio is also developing an aerosolized COVID-19 treatment inspired by llamas and is currently trying to advance its candidate into clinical trials by the end of the year. Their main candidate, VHH-72Fc was considered to bind to an epitope that is found both in SARS-CoV-2 and SARS-CoV. Yet, the llama inspired treatments are still behind antibody efforts like that of Regeneron.

Even though, there are multiple vaccines in development, researchers at UCSF believe that AeroNabs can be used as a sort of personal protective equipment until vaccines become available. The same researchers are planning human trials and are in discussion with partners who can provide manufacturing and distribution backing.

SOURCE

https://www.fiercebiotech.com/research/ucsf-engineers-develop-llama-inspired-aeronabs-to-strangle-covid-19-inhaler

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FDA Authorizes Convalescent Plasma for COVID-19 Patients

Reporter: Irina Robu, PhD

The U.S. Food and Drug Administration authorized convalescent plasma therapy in August 2020 for people with coronavirus disease 2019. The convalescent plasma shows promising efficacy in hospitalized patients with COVID-19 and the benefits outweighs the risk  and FDA gave emergency use authorization. The approval is not  for any particular convalescent plasma product, but for preparation collected by FDA registered blood establishments from individuals whose plasma contains anti-SARS-CoV-2 antibodies, and who meet all donor eligibility requirements.

What exactly is convalescent plasma ? It is blood donated from patients who have recovered from COVID-19 has antibodies to the virus that causes it. The donated blood is processed by removing blood cells, leaving behind plasma and antibodies, which can be given to people with COVID-19 to boost their ability to fight the virus. According to FDA, COVID-19 covalescent plasma with high antibody titer can be effective in reducing mortality in hospitalized patients, but low antibody titer can be used based on health care provider discretion.  FDA also indicated that COVID-19 convalescent plasma may be effective in lessening the severity or shortening the length of COVID-19 illness in some hospitalized patients.

To confirm the results, the FDA recommended randomized trialsas COVID-19 convalescent plasma does not yet describe a new standard of care based on the current available evidence.

SOURCE

https://www.medpagetoday.com/infectiousdisease/covid19/88225?xid=NL_breakingnewsalert_2020-08-23

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Coronavirus mutation-does it matter?

Reporter : Irina Robu, PhD

Soon after SARS-CoV-2 was detected in China, scientists began analyzing viral sample and posting the genetic codes online. Mutations allowed researchers to track the spread by linking closely related viruses to understand how SARS-CoV-2 infects humans.  They recognized that SARS-CoV-2 encode their genome in RNA and tends to pick up mutations quickly as they are copied inside their hosts.  Yet,  sequencing data suggest that coronaviruses change more slowly than most RNA viruses, probably because of a proofreading enzyme that corrects fatal copying mutations.  In spite of the virus slow mutation rate, scientists have been able to classified more than 12,000 mutations in SARS-CoV-2 genomes.

Many scientists such as David Montefiori, a virologist who spent much of his career studying how chance mutations in HIV helps it evade the immune system thought that COVID-19 might cause the same thing.  His laboratory in collaboration with Dr. Bette Korber investigated several thousands of coronavirus sequences for mutations that might have changed virus properties around the world.

Compared to HIV, SARS-CoV-2 seems to be changing slower than it spreads, but one mutation is obvious. That mutation  includes a gene encoding the spike protein, which helps the virus particles penetrate cells. According to Korber, the 614th amino acid position of the spike protein, the amino acid aspartate was replaced by glycine, because of a mutation, D614G that altered a single nucleotide in the virus’s 29,903-letter RNA code.

To observe whether D614G  mutation made the virus more transmissible, Montefiori evaluated its effects under laboratory conditions but he couldn’t study the natural SARS-CoV-2 virus in his lab, because of the biosafety containment required. So, he studied a genetically modified form of HIV that used the SARS-CoV-2 spike protein to infect cells. Such ‘pseudo virus’ particles are a workhorse of virology labs: they enable the safe study of deadly pathogens such as the Ebola virus, and they make it simpler to test the effects of mutations.

The strongest sign that D614G has a consequence on the spread of SARS-CoV-2 in humans comes from an ambitious UK effort called the COVID-19 Genomics UK Consortium, which has analyzed genomes of around 25,000 viral samples. From these data, researchers have identified more than 1,300 instances in which a virus entered the United Kingdom and spread, including examples of D- and G-type viruses.

What is clearly known is that D614G is an adaptation that helps the virus infect cells or compete with viruses that don’t carry the change, while at the same time altering a bit of information about how SARS-CoV-2 spreads between people and through a population.  Some scientists believe that D614G mutation should explain how SARS-CoV-2 fuses with cells and can use that process to develop a more efficient vaccine. 

At the present time, the evidence suggests that D614G doesn’t stop the immune system’s neutralizing antibodies from recognizing SARS-CoV-2, partly because the mutation is not in the spike protein’s receptor-binding domain.

SOURCE

https://www.nature.com/articles/d41586-020-02544-6?utm_source=Nature+Briefing

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Miniproteins against the COVID-19 Spike protein may be therapeutic

Reporter: Stephen J. Williams, PhD

Computer-designed proteins may protect against coronavirus

At a Glance

  • Researchers designed “miniproteins” that bound tightly to the SARS-CoV-2 spike protein and prevented the virus from infecting human cells in the lab.
  • More research is underway to test the most promising of the antiviral proteins.

 

 

 

 

 

 

 

An artist’s conception of computer-designed miniproteins (white) binding coronavirus spikes. UW Institute for Protein Design

The surface of SARS-CoV-2, the virus that causes COVID-19, is covered with spike proteins. These proteins latch onto human cells, allowing the virus to enter and infect them. The spike binds to ACE2 receptors on the cell surface. It then undergoes a structural change that allows it to fuse with the cell. Once inside, the virus can copy itself and produce more viruses.

Blocking entry of SARS-CoV-2 into human cells can prevent infection. Researchers are testing monoclonal antibody therapies that bind to the spike protein and neutralize the virus. But these antibodies, which are derived from immune system molecules, are large and not ideal for delivery through the nose. They’re also often not stable for long periods and usually require refrigeration.

Researchers led by Dr. David Baker of the University of Washington set out to design synthetic “miniproteins” that bind tightly to the coronavirus spike protein. Their study was funded in part by NIH’s National Institute of General Medical Sciences (NIGMS) and National Institute of Allergy and Infectious Diseases (NIAID). Findings appeared in Science on September 9, 2020.

The team used two strategies to create the antiviral miniproteins. First, they incorporated a segment of the ACE2 receptor into the small proteins. The researchers used a protein design tool they developed called Rosetta blueprint builder. This technology allowed them to custom build proteins and predict how they would bind to the receptor.

The second approach was to design miniproteins from scratch, which allowed for a greater range of possibilities. Using a large library of miniproteins, they identified designs that could potentially bind within a key part of the coronavirus spike called the receptor binding domain (RBD). In total, the team produced more than 100,000 miniproteins.

Next, the researchers tested how well the miniproteins bound to the RBD. The most promising candidates then underwent further testing and tweaking to improve binding.

Using cryo-electron microscopy, the team was able to build detailed pictures of how two of the miniproteins bound to the spike protein. The binding closely matched the predictions of the computational models.

Finally, the researchers tested whether three of the miniproteins could neutralize SARS-CoV-2. All protected lab-grown human cells from infection. Candidates LCB1 and LCB3 showed potent neutralizing ability. These were among the designs created from the miniprotein library. Tests suggested that these miniproteins may be more potent than the most effective antibody treatments reported to date.

“Although extensive clinical testing is still needed, we believe the best of these computer-generated antivirals are quite promising,” says Dr. Longxing Cao, the study’s first author. “They appear to block SARS-CoV-2 infection at least as well as monoclonal antibodies but are much easier to produce and far more stable, potentially eliminating the need for refrigeration.”

Notably, this study demonstrates the potential of computational models to quickly respond to future viral threats. With further development, researchers may be able to generate neutralizing designs within weeks of obtaining the genome of a new virus.

—by Erin Bryant

Source: https://www.nih.gov/news-events/nih-research-matters/computer-designed-proteins-may-protect-against-coronavirus

Original article in Science

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

 

  1. View ORCID ProfileLongxing Cao1,2
  2. Inna Goreshnik1,2
  3. View ORCID ProfileBrian Coventry1,2,3
  4. View ORCID ProfileJames Brett Case4
  5. View ORCID ProfileLauren Miller1,2
  6. Lisa Kozodoy1,2
  7. Rita E. Chen4,5
  8. View ORCID ProfileLauren Carter1,2
  9. View ORCID ProfileAlexandra C. Walls1
  10. Young-Jun Park1
  11. View ORCID ProfileEva-Maria Strauch6
  12. View ORCID ProfileLance Stewart1,2
  13. View ORCID ProfileMichael S. Diamond4,7
  14. View ORCID ProfileDavid Veesler1
  15. View ORCID ProfileDavid Baker1,2,8,*

See all authors and affiliations

Science  09 Sep 2020:
eabd9909
DOI: 10.1126/science.abd9909

Abstract

Targeting the interaction between the SARS-CoV-2 Spike protein and the human ACE2 receptor is a promising therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer generated scaffolds were either built around an ACE2 helix that interacts with the Spike receptor binding domain (RBD), or docked against the RBD to identify new binding modes, and their amino acid sequences designed to optimize target binding, folding and stability. Ten designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked ARS-CoV-2 infection of Vero E6 cells with IC 50 values between 24 pM and 35 nM; The most potent, with new binding modes, are 56 and 64 residue proteins (IC 50 ~ 0.16 ng/ml). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.

 

RESEARCH ARTICLE

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

  1. View ORCID ProfileLongxing Cao1,2
  2. Inna Goreshnik1,2
  3. View ORCID ProfileBrian Coventry1,2,3
  4. View ORCID ProfileJames Brett Case4
  5. View ORCID ProfileLauren Miller1,2
  6. Lisa Kozodoy1,2
  7. Rita E. Chen4,5
  8. View ORCID ProfileLauren Carter1,2
  9. View ORCID ProfileAlexandra C. Walls1
  10. Young-Jun Park1
  11. View ORCID ProfileEva-Maria Strauch6
  12. View ORCID ProfileLance Stewart1,2
  13. View ORCID ProfileMichael S. Diamond4,7
  14. View ORCID ProfileDavid Veesler1
  15. View ORCID ProfileDavid Baker1,2,8,*

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Science  09 Sep 2020:
eabd9909
DOI: 10.1126/science.abd9909

Abstract

Targeting the interaction between the SARS-CoV-2 Spike protein and the human ACE2 receptor is a promising therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer generated scaffolds were either built around an ACE2 helix that interacts with the Spike receptor binding domain (RBD), or docked against the RBD to identify new binding modes, and their amino acid sequences designed to optimize target binding, folding and stability. Ten designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked ARS-CoV-2 infection of Vero E6 cells with IC 50 values between 24 pM and 35 nM; The most potent, with new binding modes, are 56 and 64 residue proteins (IC 50 ~ 0.16 ng/ml). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.

 

SARS-CoV-2 infection generally begins in the nasal cavity, with virus replicating there for several days before spreading to the lower respiratory tract (1). Delivery of a high concentration of a viral inhibitor into the nose and into the respiratory system generally might therefore provide prophylactic protection and/or therapeutic benefit for treatment of early infection, and could be particularly useful for healthcare workers and others coming into frequent contact with infected individuals. A number of monoclonal antibodies are in development as systemic treatments for COVID-19 (26), but these proteins are not ideal for intranasal delivery as antibodies are large and often not extremely stable molecules and the density of binding sites is low (two per 150 KDa. antibody); antibody-dependent disease enhancement (79) is also a potential issue. High-affinity Spike protein binders that block the interaction with the human cellular receptor angiotensin-converting enzyme 2 (ACE2) (10) with enhanced stability and smaller sizes to maximize the density of inhibitory domains could have advantages over antibodies for direct delivery into the respiratory system through intranasal administration, nebulization or dry powder aerosol. We found previously that intranasal delivery of small proteins designed to bind tightly to the influenza hemagglutinin can provide both prophylactic and therapeutic protection in rodent models of lethal influenza infection (11).

Design strategy

We set out to design high-affinity protein minibinders to the SARS-CoV-2 Spike RBD that compete with ACE2 binding. We explored two strategies: first we incorporated the alpha-helix from ACE2 which makes the majority of the interactions with the RBD into small designed proteins that make additional interactions with the RBD to attain higher affinity (Fig. 1A). Second, we designed binders completely from scratch without relying on known RBD-binding interactions (Fig. 1B). An advantage of the second approach is that the range of possibilities for design is much larger, and so potentially a greater diversity of high-affinity binding modes can be identified. For the first approach, we used the Rosetta blueprint builder to generate miniproteins which incorporate the ACE2 helix (human ACE2 residues 23 to 46). For the second approach, we used RIF docking (12) and design using large miniprotein libraries (11) to generate binders to distinct regions of the RBD surface surrounding the ACE2 binding site (Fig. 1 and fig. S1).

 

 

 

 

 

 

 

 

 

 

 

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Fig. 1 Overview of the computational design approaches.

(A) Design of helical proteins incorporating ACE2 helix. (B) Large scale de novo design of small helical scaffolds (top) followed by rotamer interaction field (RIF) docking to identify shape and chemically complementary binding modes.

For full article please  go to Science at https://science.sciencemag.org/content/early/2020/09/08/science.abd9909

 

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